The movie is based around the concept of an Earth-like planet where humans never existed and anthropomorphicanimals are the main, evolved sentient beings. Most of the story takes place in the animal city of Zootopia, whose motto is "Anyone can be Anything", and which is divided by neighborhoods like Tundratown, Sahara Square, Little Rodentia, the Rainforest District, and Savanna Central, a virtual melting pot where animals from every environment live together. However, the city is separated into classes, where they face prejudice based on preconceived notions about their species. Although it's been thousands of years since the animals of Zootopia have evolved beyond their savage ways where predators hunted and prey lived in fear, there is still some lingering unease over their respective natures.

Judy Hopps grew up in the nearby town of Bunnyburrow among a family of carrot farmers but dreams of being the first ever bunny cop in Zootopia. She goes to the police academy where after some struggles she graduates at the top of her class and gets a warm welcome from Zootopia mayor Lionheart into the police department. Chief Bogo, unaccustomed to having anything other than larger animals in his force, assigns Judy to parking duty while the others are sent to work on the cases of fourteen missing mammals, all predators. Though disappointed to be treated as a token bunny, Judy is determined to excel at her task. She has her first encounter with Nick Wilde, whom she aids when he and his toddler is being refused service at an ice cream parlor for elephants, but she soon discovers Nick is a wily, fast-talking con artist and the "toddler" is Finnick, a full-grown fennec.

On her second day at work, Judy witnesses a burglary in progress and abandons her parking duty to chase the thief, Duke Weaselton, into Little Rodentia. But when the booty turns out to be nothing but a bunch of flower bulbs, Chief Bogo is ready to fire Judy on the spot, but a timely appearance by assistant mayor Bellwhether and Mrs. Otterton, wife of one of the missing mammals, results in Judy being given 48 hours to solve the case.

Judy has little to go on but sees Nick in the last known picture of Mr. Otterton, so she tracks him down and by recording a few confessions on her carrot pen, convinces him to aid her in finding him. Their search first takes them to Yax, leader of a naturalist colony, where they get the license number of the vehicle Otterton was last seen in, then to the DMV which turns out to be staffed entirely by sloths. They find the vehicle, a limo, which Nick discovers belongs to Mr. Big, the most feared crime boss in Tundratown. They are accosted by some of Mr. Big's thugs and taken to him, an arctic shrew. Mr. Big is about to "ice" them when his daughter reveals Judy has saved her from being smashed by a giant donut during the earlier chase in Little Rodentia. They are invited to stay for the daughter's wedding, and are told that the limo was being driven by a jaguar named Manchas. Nick and Judy visit Manchas at his home in the Rainforest District, and he tells of how Mr. Otterton went savage and attacked him. While they are talking, Manchas himself goes savage and a chase ensues, ending with Manchas chained and Nick and Judy bound awkwardly.

The police and Chief Bogo arrive to find them this way, but Manchas has mysteriously disappeared, and Bogo is about to fire Judy on the spot, but Nick steps in and says they have ten hours left to find the missing otter. They head off together and Nick tells the story of how he was bullied as a child for being a predator and a fox, an experience that made Nick decide he may as well be what people expect of him. Nick suggests they view traffic camera footage to discover what happened to Manchas, and Judy contacts Bellwether to gain access to the system. They discover Manchas was taken by two wolves, "night howlers", who took him to an asylum. Nick and Judy go and break into the place, where they discover all the missing mammals, including Mr. Otterton and Manchas, all of whom have gone savage. They overhear a conversation between mayor Lionheart and a doctor before an alarm goes off and they barely escape with the evidence. The police swarm the place and arrest Lionheart.

Judy invites Nick to become a cop and be her partner, but she says some wrong things leading to fears that any predator may be at risk of turning savage. Nick walks out on her, unrest increases among the animals of Zootopia, and pop singer Gazelle leads a peaceful protest to bring back the Zootopia she loves. Bellwether, now mayor, and Chief Bogo offer Judy a role as the public face of the police department, but Judy, dismayed by what has happened, resigns from the police force. Back in Bunnyburrow, Judy is selling carrots from the farm when an encounter with a former bully turned pastry chef reveals that the flowers they use to keep bugs away, and which once caused her uncle to go crazy, are called "night howlers".

She rushes back to Zootopia where she finds Nick, apologizes to him for what she said earlier in the press conference, and tells what she learned. They find Weaselton, who eventually reveals he was stealing the bulbs for a secret laboratory. Nick and Judy find the lab, run by rams, in an abandoned tram car, where night howlers are being grown and turned into a serum to make animals go savage. They steal the tram, which turns out to be still operable, but in their escape end up destroying all the evidence except a case with a dart gun and a few of the serum pellets. They take a short cut through the natural history museum on the way to the ZPD, where they encounter Mayor Bellwether, whom Judy quickly works out is behind the scheme. In ensuing chase, Nick and Judy end up trapped in a display, where Bellwether reveals her plan to incite fear of predators in the majority prey population. She then shoots Nick, who turns savage and attacks Judy. Before killing her, he stops and reveals they had replaced the serum pellets in the gun with blueberries, and had also recorded Bellwether's confession on the carrot pen. The police arrive and Bellwether and her rams are arrested.

Judy reclaims her place on the ZPD and Nick joins the force, becoming her partner. The film ends with a Gazelle concert.

Release of the trailers sparked several discussions on furry forums about whether the makers were showing tacit awareness of furry fandom; possibly true due to the highlighting of the word "anthropomorphic" in the trailer (which no other movie needed to define).

In December 2015, tech and culture blog Inverse speculated that the Zootopia marketing was directed at furries. Author Emily Gaudette's article "Disney Prepares to Cash In on the Furry Demographic with 'Zootopia'"[8] quoted Reddit discussion by furries including Patch O'Furr, who was covering it at Dogpatch Press.[9]

With the release of the movie in March 2016, Gaudette wrote a second article proposing that "'Zootopia' is a Deliberate, Definitive, and Probably Sensual Fantasy for Furries".[10] It led a wave of notice a day later, when BuzzFeed’s Katie Notopoulos[11] "uncovered proof that at least one marketing agency hired by Disney to promote the film is reaching out to the furry community"[12]. Articles appeared on Gizmodo and Inquisitr[13], while Canada's National Post[14] and Vanity Fair[15] linked back to Patch O'Furr's coverage of furry meets for Zootopia at Dogpatch Press. Patch reported that his article had more views than any other in 2 years of the furry news site's history.

Furry Twitter discussion[16][17] focused on media highlighting of sex and porn, treating it in a somewhat dishonest and sensationalist manner. Emily Gaudette's initial coverage mentioned porn, however her followup reported furry criticism, and took care to moderate the topic away from sex and towards romantic chemistry. She mentioned that she was personally into the chemistry and understood how it caused "furry awakenings", and she researched and engaged with comments from furries. Followups from Buzzfeed, Gizmodo and Vanity Fair piggybacked on the initial story without researching or engaging, instead slanting coverage with links to "TonyTigerGate"[18] and Vanity Fair's hated 2001 "Pleasures of the Fur" article.